Contacts of the helix formed by residues 82 - 104 (chain D) in PDB entry 4BL5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 82 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B GLN* 3.2 12.1 - - + -
72D MET* 4.8 6.5 - - + -
78D ARG* 3.1 42.7 + - + +
79D ASN 3.0 5.5 + - - -
81D LYS* 1.3 111.4 - - + +
83D ASN* 1.3 65.5 - - - +
84D LEU 3.0 4.0 + - - -
85D ASP* 3.2 22.9 + - + +
86D PHE* 3.1 29.2 + - + -
184D ASP* 5.3 4.0 - - - -
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Residues in contact with ASN 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ALA* 4.3 7.2 - - + +
159B GLN* 4.6 4.7 + - + +
160B GLN* 3.1 4.7 + - + +
79D ASN* 3.3 11.3 + - - +
80D ILE* 4.3 7.7 + - - +
81D LYS 3.8 1.6 + - - -
82D TYR* 1.3 74.8 - - - +
84D LEU* 1.3 57.0 + - - +
86D PHE* 4.0 4.3 - - - +
87D TRP* 3.1 27.5 + - - +
138D ASN 3.8 2.8 + - - -
139D SER* 3.4 17.6 + - - +
140D ASN* 3.3 6.1 - - - -
141D PHE* 3.0 46.8 + - + -
142D GLY* 2.9 29.9 + - - +
143D TYR 4.5 0.7 + - - -
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Residues in contact with LEU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B HIS* 4.9 5.8 - - + -
153B GLN* 4.6 0.9 - - - +
156B ALA* 3.7 29.5 - - + +
157B TYR* 3.8 46.7 - - + +
160B GLN* 2.8 27.3 + - + +
161B TYR* 4.1 15.5 - - + +
83D ASN* 1.3 70.8 - - - +
85D ASP* 1.3 65.0 + - - +
87D TRP* 3.4 7.3 + - + +
88D ARG* 2.7 63.9 + - + +
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Residues in contact with ASP 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLN* 2.9 28.9 + - - -
161B TYR* 4.6 5.4 + - - -
72D MET* 3.7 23.8 - - + -
82D TYR* 3.2 15.8 + - + +
84D LEU* 1.3 81.2 - - - +
86D PHE* 1.3 62.3 + - - +
88D ARG* 4.2 5.5 + - - +
89D LYS* 2.7 46.7 + - + +
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Residues in contact with PHE 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D MET* 2.9 51.5 - - + -
73D VAL* 3.8 6.1 - - - -
74D GLY 3.9 4.7 - - - -
78D ARG* 3.8 31.0 - - + -
79D ASN* 3.4 55.0 - - - -
82D TYR* 3.1 29.7 + - + +
83D ASN* 4.0 4.5 - - - +
85D ASP* 1.3 77.5 - - - +
87D TRP* 1.3 64.3 + - - +
90D ASN* 3.0 26.1 + - - +
143D TYR* 3.8 30.7 - + + +
146D ALA* 4.4 0.7 - - - +
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Residues in contact with TRP 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TRP* 4.9 2.7 - + - -
91B VAL* 5.2 8.1 - - + -
95B ASP* 4.9 8.1 + - - +
149B MET* 3.2 57.9 - - + -
152B VAL* 4.3 10.5 - - + -
153B GLN* 4.4 20.5 - - + +
156B ALA* 5.3 3.1 - - + -
83D ASN 3.1 19.7 + - - +
84D LEU* 3.6 8.7 - - + +
86D PHE* 1.3 76.5 - - - +
88D ARG* 1.3 84.0 + - + +
91D VAL* 3.1 57.3 + - + +
142D GLY* 3.7 32.8 - - - -
145D TYR* 3.8 7.0 - - + -
146D ALA* 3.8 17.3 - - - +
149D MET* 4.2 6.3 - - + -
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Residues in contact with ARG 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ASP* 2.5 52.0 + - - +
99B HIS* 3.4 43.1 + - - +
153B GLN* 6.4 0.2 - - + -
157B TYR* 3.4 22.4 - - + -
84D LEU* 2.7 39.6 + - + +
85D ASP* 4.2 3.4 - - - +
87D TRP* 1.3 88.7 - - + +
89D LYS* 1.3 63.8 + - + +
91D VAL* 3.8 2.4 + - - +
92D HIS* 3.4 46.9 + - - -
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Residues in contact with LYS 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D THR* 3.7 17.1 - - + +
72D MET* 3.5 34.5 - - + -
85D ASP* 2.7 30.7 + - + +
88D ARG* 1.3 72.4 - - + +
90D ASN* 1.3 56.3 + - - +
92D HIS* 3.5 3.8 + - - +
93D MET* 3.2 44.1 + - + +
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Residues in contact with ASN 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ALA 4.7 0.2 - - - +
71D ALA* 2.9 19.0 - - - +
72D MET* 2.7 49.5 + - - +
86D PHE* 3.0 25.1 + - - +
89D LYS* 1.3 75.8 - - - +
91D VAL* 1.3 60.3 + - - +
93D MET* 3.7 4.5 - - - +
94D ASN* 2.9 42.6 + - - +
143D TYR* 3.7 19.8 + - - +
146D ALA* 3.9 13.5 - - + -
147D LYS* 5.4 3.4 - - - -
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Residues in contact with VAL 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TRP* 5.5 5.8 - - + -
91B VAL* 4.1 26.0 - - + -
95B ASP* 6.2 2.7 - - + -
87D TRP* 3.1 60.8 + - + +
88D ARG* 4.1 3.8 - - - +
90D ASN* 1.3 72.7 - - - +
92D HIS* 1.3 70.2 + - + +
94D ASN* 3.8 5.6 - - - +
95D ASP* 2.9 34.9 + - + +
146D ALA* 4.1 9.4 - - + +
149D MET* 5.6 3.8 - - + -
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Residues in contact with HIS 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B HIS* 5.7 9.4 - + - -
95B ASP* 2.4 34.1 + - + -
96B ASN* 5.5 1.0 + - - -
49D THR* 3.9 31.0 + - - +
88D ARG* 3.4 41.5 + - - -
89D LYS* 3.5 8.5 + - - +
90D ASN 3.3 0.6 - - - -
91D VAL* 1.3 85.1 - - + +
93D MET* 1.3 64.3 + - - +
95D ASP* 3.8 3.7 - - + +
96D ASN* 2.9 35.9 + - - +
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Residues in contact with MET 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ASP* 6.0 0.2 - - - +
48D LEU* 3.2 40.6 + - + -
49D THR* 3.7 10.1 - - + -
68D HIS* 4.6 2.0 - - + -
70D ALA* 4.0 15.3 - - - +
71D ALA* 3.9 14.8 - - - -
72D MET* 3.6 26.7 - - + +
89D LYS* 3.2 34.4 + - + +
90D ASN* 3.7 10.3 - - - +
92D HIS* 1.3 78.9 - - - +
94D ASN* 1.3 61.3 + - - +
96D ASN* 3.8 0.7 - - - +
97D VAL* 2.9 36.6 + - - +
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Residues in contact with ASN 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D HIS* 2.7 35.2 + - + -
70D ALA 4.2 5.4 - - - +
71D ALA* 5.4 0.3 - - - +
90D ASN* 2.9 36.6 + - - +
91D VAL* 3.8 5.3 - - - +
93D MET* 1.3 74.9 - - - +
95D ASP* 1.3 65.4 + - - +
97D VAL* 3.9 0.2 - - - +
98D LEU* 3.1 36.8 + - + +
146D ALA* 3.9 12.5 + - - +
147D LYS* 4.9 5.6 + - - +
150D ILE* 3.4 38.3 - - + +
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Residues in contact with ASP 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TRP* 4.9 5.4 + - - +
88B ARG* 2.7 39.5 + - - +
91B VAL* 6.3 2.5 - - + -
92B HIS* 2.6 33.3 + - + -
91D VAL* 2.9 28.0 + - + +
92D HIS* 3.8 4.9 - - + +
94D ASN* 1.3 72.1 - - - +
96D ASN* 1.3 59.9 + - - +
98D LEU* 4.2 3.3 - - - +
99D HIS* 2.9 39.2 + - - +
157D TYR* 4.6 1.0 + - - -
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Residues in contact with ASN 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B HIS* 5.4 1.4 + - - -
48D LEU 3.3 21.7 + - - +
49D THR 3.4 21.4 + - - -
50D ASP 3.6 2.6 + - - -
51D THR* 2.9 37.4 + - - +
54D THR* 3.3 15.7 - - + +
92D HIS* 2.9 24.6 + - - +
95D ASP* 1.3 80.2 - - - +
97D VAL* 1.3 61.0 + - - +
99D HIS* 4.8 3.4 - - - -
100D SER* 2.6 33.1 + - - +
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Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D THR* 4.4 5.4 - - + -
48D LEU* 3.7 31.4 - - + -
54D THR* 4.2 4.7 - - + -
58D PHE* 3.7 17.7 - - + -
66D VAL* 4.5 5.2 - - + -
68D HIS* 3.5 48.9 - - + +
93D MET 2.9 27.1 + - - +
94D ASN 3.3 2.2 + - - +
96D ASN* 1.3 73.4 - - - +
98D LEU* 1.3 59.9 - - + +
100D SER* 3.2 2.9 + - - -
101D ALA* 2.8 35.6 + - + +
109D VAL* 5.3 1.6 - - + -
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Residues in contact with LEU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D HIS* 5.4 1.1 - - + -
94D ASN* 3.1 24.1 + - + +
95D ASP* 4.2 3.4 - - - +
97D VAL* 1.3 79.9 - - + +
99D HIS* 1.3 58.0 + - - +
101D ALA* 3.2 6.3 + - - +
102D PHE* 2.8 30.0 + - - +
109D VAL* 3.7 28.7 - - + -
111D SER* 4.1 12.1 - - - +
150D ILE* 4.7 10.5 - - + +
153D GLN* 3.8 29.8 - - + -
154D ASN* 4.1 19.1 - - - +
157D TYR* 3.9 17.7 - - + -
165D PHE* 3.8 12.6 - - + -
166D THR 6.1 0.4 - - - +
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Residues in contact with HIS 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 5.0 4.9 - - + -
88B ARG* 3.4 43.9 + - - +
95D ASP 2.9 24.3 + - - +
96D ASN* 4.7 3.1 - - - +
98D LEU* 1.3 73.7 - - - +
100D SER* 1.3 61.1 + - - +
102D PHE* 3.6 23.0 - + - +
103D GLU* 3.2 47.2 + - - +
157D TYR* 2.6 28.6 + + - +
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Residues in contact with SER 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D THR* 5.1 1.2 + - - +
54D THR* 3.7 8.3 - - - +
55D ARG* 3.8 20.9 + - - +
58D PHE* 3.6 33.0 - - - +
96D ASN* 2.6 24.8 + - - +
97D VAL 3.7 1.6 - - - -
99D HIS* 1.3 76.1 - - - +
101D ALA* 1.3 66.1 + - - +
103D GLU* 3.0 11.6 + - - +
104D VAL* 3.0 24.1 + - - +
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Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D PHE* 3.4 21.4 - - + -
66D VAL* 4.2 5.6 - - + -
97D VAL* 2.8 18.9 + - + +
98D LEU* 3.4 9.0 - - - +
100D SER* 1.3 72.2 - - - +
102D PHE* 1.3 63.4 + - - +
104D VAL* 3.5 2.5 + - - +
105D GLY 3.1 3.8 + - - -
106D ALA* 3.0 29.4 + - + +
109D VAL* 3.5 32.5 - - + -
165D PHE* 4.5 0.7 - - - -
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Residues in contact with PHE 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 6.3 0.4 - - + -
98D LEU 2.8 20.1 + - - +
99D HIS* 3.6 29.6 - + - +
101D ALA* 1.3 73.1 - - - +
103D GLU* 1.3 67.3 + - + +
105D GLY* 3.0 19.2 + - - -
106D ALA 5.0 0.4 - - - +
157D TYR* 3.8 19.7 - + + -
161D TYR* 3.7 58.8 - + + -
163D CYS* 3.8 19.3 - - - -
165D PHE* 3.9 11.3 - - + -
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Residues in contact with GLU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ARG* 2.8 48.8 + - - +
99D HIS* 3.2 42.4 + - - +
100D SER* 3.0 11.3 + - - +
102D PHE* 1.3 83.8 - - + +
104D VAL* 1.3 57.5 + - - +
105D GLY* 3.1 5.2 + - - -
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Residues in contact with VAL 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ARG* 5.1 6.8 - - - +
58D PHE* 4.1 25.6 - - + +
62D GLN* 4.9 15.4 - - - +
63D PRO* 4.7 15.6 - - + +
100D SER 3.0 16.3 + - - +
101D ALA 4.0 3.4 - - - +
103D GLU* 1.3 75.4 - - - +
105D GLY* 1.3 60.9 + - - +
106D ALA* 3.4 2.5 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il